Hi Salil - I'm cc-ing Doug who may be able to help. The error happens when bbregister invokes fslregister, in this particular line of fslregister: set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
When run on brainmask.mgz, it returns "ERROR: could not determine file".
a.y
On Wed, 6 Mar 2013, Salil Soman wrote:
Thank you for your email. Changing the mask option got me past the error I was having initially, but now I get these new errors:
mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis ter.30396/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis ter.30396/fslregister/refvol.fslregister.nii
Thank you for your consideration.
Best wishes,
-S
On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Salil - The problem is that you've set dob0 = 1 but you haven't set b0mlist and b0plist, so it doesn't know where to find your field maps to do the B0 unwarping.
a.y
Salil, can you run fslregister with --debug as the first option, capture the terminal output, and send it to me? thanks doug
On 03/07/2013 09:02 PM, Anastasia Yendiki wrote:
Hi Salil - I'm cc-ing Doug who may be able to help. The error happens when bbregister invokes fslregister, in this particular line of fslregister: set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
When run on brainmask.mgz, it returns "ERROR: could not determine file".
a.y
On Wed, 6 Mar 2013, Salil Soman wrote:
Thank you for your email. Changing the mask option got me past the error I was having initially, but now I get these new errors:
mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
ter.30396/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
ter.30396/fslregister/refvol.fslregister.nii
Thank you for your consideration.
Best wishes,
-S
On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Salil - The problem is that you've set dob0 = 1 but you haven't set b0mlist and b0plist, so it doesn't know where to find your field maps to do the B0 unwarping.
a.y
Hi Doug,
I think I am having the same problem, but only when running on our Red Hut cluster (CentOS 6 was fine). I have attached the terminal output with --debug
Many thanks,
- Charles
On 9 March 2013 03:47, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Salil, can you run fslregister with --debug as the first option, capture the terminal output, and send it to me? thanks doug
On 03/07/2013 09:02 PM, Anastasia Yendiki wrote:
Hi Salil - I'm cc-ing Doug who may be able to help. The error happens when bbregister invokes fslregister, in this particular line of fslregister: set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
When run on brainmask.mgz, it returns "ERROR: could not determine file".
a.y
On Wed, 6 Mar 2013, Salil Soman wrote:
Thank you for your email. Changing the mask option got me past the error I was having initially, but now I get these new errors:
mri_convert ERROR: could not determine file for
/mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
ter.30396/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for
/mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
ter.30396/fslregister/refvol.fslregister.nii
Thank you for your consideration.
Best wishes,
-S
On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Salil - The problem is that you've set dob0 = 1 but you haven't set b0mlist and b0plist, so it doesn't know where to find your field maps to do the B0 unwarping.
a.y
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Charles, can you verify that brainmask.mgz exists for that subject? What do you get if you run stem2fname $SUBJECTS_DIR/$subject/mri/brainmask
doug
On 3/11/13 4:07 AM, Charles Malpas wrote:
Hi Doug,
I think I am having the same problem, but only when running on our Red Hut cluster (CentOS 6 was fine). I have attached the terminal output with --debug
Many thanks,
- Charles
On 9 March 2013 03:47, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Salil, can you run fslregister with --debug as the first option, capture the terminal output, and send it to me? thanks doug On 03/07/2013 09:02 PM, Anastasia Yendiki wrote: > > Hi Salil - I'm cc-ing Doug who may be able to help. The error happens > when bbregister invokes fslregister, in this particular line of > fslregister: > set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol` > > When run on brainmask.mgz, it returns "ERROR: could not determine file". > > a.y > > On Wed, 6 Mar 2013, Salil Soman wrote: > >> >> Thank you for your email. Changing the mask option got me past the >> error I >> was having initially, but now I get these new errors: >> >> mri_convert ERROR: could not determine file for >> /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis >> >> ter.30396/fslregister/refvol.fslregister.nii >> mri_convert ERROR: could not determine file for >> /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis >> >> ter.30396/fslregister/refvol.fslregister.nii >> >> Thank you for your consideration. >> >> Best wishes, >> >> -S >> >> On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki >> <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> wrote: >> >> Hi Salil - The problem is that you've set dob0 = 1 but you haven't set >> b0mlist and b0plist, so it doesn't know where to find your field maps >> to do >> the B0 unwarping. >> >> a.y >> >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- *Charles Malpas * Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010
*Melbourne Brain Centre @ RMH* Neuropsychiatry Research Group** Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas@student.unimelb.edu.au mailto:c.malpas@student.unimelb.edu.au Skype: charles.malpas
Hi Doug,
The brainmask.mgz does exists, and the full recon-all runs normally. The problem seems to be in the -FLAIRpial sequence only for me. The registration runs, but doesn't produce mri/FLAIR.mgz.
I have attached the FLAIRraw.dat.log file. Please let me know if you would like me to upload the subjects dir.
Kind regards,
- Charles
On 11 March 2013 19:53, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Charles, can you verify that brainmask.mgz exists for that subject? What do you get if you run stem2fname $SUBJECTS_DIR/$subject/mri/brainmask
doug
On 3/11/13 4:07 AM, Charles Malpas wrote:
Hi Doug,
I think I am having the same problem, but only when running on our Red Hut cluster (CentOS 6 was fine). I have attached the terminal output with --debug
Many thanks,
- Charles
On 9 March 2013 03:47, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Salil, can you run fslregister with --debug as the first option, capture the terminal output, and send it to me? thanks doug
On 03/07/2013 09:02 PM, Anastasia Yendiki wrote:
Hi Salil - I'm cc-ing Doug who may be able to help. The error happens when bbregister invokes fslregister, in this particular line of fslregister: set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
When run on brainmask.mgz, it returns "ERROR: could not determine file".
a.y
On Wed, 6 Mar 2013, Salil Soman wrote:
Thank you for your email. Changing the mask option got me past the error I was having initially, but now I get these new errors:
mri_convert ERROR: could not determine file for
/mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
ter.30396/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for
/mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
ter.30396/fslregister/refvol.fslregister.nii
Thank you for your consideration.
Best wishes,
-S
On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Salil - The problem is that you've set dob0 = 1 but you haven't set b0mlist and b0plist, so it doesn't know where to find your field maps to do the B0 unwarping.
a.y
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- *Charles Malpas * Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010
*Melbourne Brain Centre @ RMH* Neuropsychiatry Research Group* * Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas@student.unimelb.edu.au Skype: charles.malpas
freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Charles Malpas -
Douglas Greve -
Douglas N Greve